Thanks for the response - I'm on a slow enough connection that I decided that I didn't want to go through the process of clicking the fix button one-by-one, so I just added the "fix all" button myself. :)
In the process, I got a little carried away and decided to reformat the code to add a better message display function, move some of the duplicate code into functions for code reuse, and reformat all of the code to meet the WordPress coding standards (found at http://codex.wordpress.org/WordPress_Coding_Standards).
Here's a link to the changed version: http://cl.ly/2b2I2a420k2m0v1N3M3m
Feel free to add any/all/none of that code to the next version of the plugin. I'd be really happy if I was able to help make your very useful plugin even more useful to people like me with large multisite installs (with 100s of themes and old timthumb files).
So, I'm basically giving you that modified code for you to use/discard as you see fit. :)
I'll be installing it on my multisite install.
Keep up the good work!
P.S. Side question - does Locker work with multisite? If so, does one multisite install count as one site toward the plan quota?